User: Sudosundu

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Sudosundu0
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Posts by Sudosundu

<prev • 8 results • page 1 of 1 • next >
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Nanopolish makerange for smaller contigs
... My aim is to characterize plant viral genome from nanopore reads. I am doing reference based assembly. First mapping the reads to the reference genome with minimap2 and polishing with nanopolish. In nanopolish variants, the reference file which I have to use contains 3 contigs For example ...
genome assembly written 3 months ago by Sudosundu0
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Nanopolish variant calling. Need to specify input region of the reference genome
... I mapped the reads with the reference fasta with minimap2. Out put: BAM file Then I used the BAM, reference fasta, reads to nanopolish variant calling. And I got this error. Error: genome has multiple contigs, please use -w to specify input region My reference fasta contains 6 fasta sequences. ...
genome assembly written 3 months ago by Sudosundu0 • updated 3 months ago by WouterDeCoster43k
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Comment: C: Reference sequence to be used for assembly in nanopore
... Now I am using the reference genome from the NCBI. ...
written 3 months ago by Sudosundu0
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Comment: C: Reference sequence to be used for assembly in nanopore
... Hi, I just came through your Nanopack. Thanks for the pack. My final aim is to characterise the plant viral genome. I am sequenced virus infected plant samples and to characterize them based on a reference viral genome. ...
written 3 months ago by Sudosundu0
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Comment: C: Reference sequence to be used for assembly in nanopore
... Hi Sorry for the less information. I am working on plant virus. My aim is to characterize the viral genome. Refseq DNA file means reference genome to be used for mapping the reads. https://www.ncbi.nlm.nih.gov/refseq/ ...
written 3 months ago by Sudosundu0
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NCBI workbench for Ubuntu 16.04
... Where can I found the NCBI workbench for Ubuntu 16.04. I do not know which package to be used for 16.04 LTS. Please help ...
sequencing written 4 months ago by Sudosundu0 • updated 4 months ago by genomax84k
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How to trim Nanopore reads. Please suggest a tool.
... Hi all, I checked the Nanopore basecalled reads using MinION QC tool. From what I've understand, I need to select only the reads which are passed the N50 value. MinION QC gives the information only. Now how to select those passed reads from the data. Which tool to be used to select the best quality ...
minionqc nanopore ont written 4 months ago by Sudosundu0 • updated 4 months ago by genomax84k
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Reference sequence to be used for assembly in nanopore
... Hello, I am a newbie in NGS data analysis. I wanted to analyse the Oxford nanopore's reads. For assembly I am using minimap tool. A reference file is needed for the process. Can I use any related/similar fasta sequence as a reference file or I must use only the Refseq DNA file? Need some help! ...
assembly reference written 5 months ago by Sudosundu0

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